GEP5 model for multiple myeloma

Abstract

The invention provides, inter alia, methods of prognosing a subject with, or suspected of having, multiple myeloma. In certain embodiments, the methods entail testing the gene expression levels of enolase 1 (ENO1), fatty acid binding protein 5 (FABP5), thyroid hormone receptor interactor 13 (TRIP 13), transgelin 2 (TAGLN2), and replication factor C (activator 1) 4 (RFC4) in a biological sample isolated from the subject. The invention also provides methods of treatment for multiple myeloma, as well as kits, oligonucleotides, and systems for performing the methods provided by the invention.

What is claimed is: 
     
       1. A method of prognosing a subject suspected of having multiple myeloma, comprising:
 testing the gene expression levels of enolase 1 (ENO1), fatty acid binding protein 5 (FABP5), thyroid hormone receptor interactor 13 (TRIP13), transgelin 2 (TAGLN2), and replication factor C (activator 1) 4 (RFC4) in a biological sample isolated from the subject using a method that detects gene expression levels when the biological sample comprises about 50,000 or fewer myeloma cells; and 
 quantifying the gene expression levels of each of ENO1, FABP5, TRIP13, TAGLN2, and RFC4, 
 wherein an elevated mean, log-normalized gene expression level of ENO1, FABP5, TRIP13, TAGLN2, and RFC4 as compared to a suitable control for each gene is associated with a poor prognosis for the subject. 
 
     
     
       2. The method of  claim 1 , wherein the poor prognosis is reduced likelihood of overall survival (OS) and/or reduced likelihood of progression-free survival (PFS). 
     
     
       3. The method of  claim 1 , wherein the gene expression levels are tested at the protein level or at the nucleic acid level. 
     
     
       4. The method of  claim 1 , wherein the gene expression levels are tested at the nucleic acid level. 
     
     
       5. The method of  claim 4 , wherein the gene expression levels are tested by quantitative polymerase chain reaction (qPCR), quantitative real-time polymerase chain reaction (qRTPCR), digital droplet PCR, (ddPCR), sequencing, northern blotting, or Southern blotting. 
     
     
       6. The method of  claim 5 , wherein the gene expression levels are tested by qRTPCR. 
     
     
       7. The method of  claim 6 , wherein the gene expression levels are tested by qRTPCR comprising the use of sets of three primers for each of the genes, wherein for each set of three primers at least one of the primers is detectably labeled and is subject to polymerase-dependent hydrolysis in the presence of the target template of the set of three primers. 
     
     
       8. The method of  claim 7 , wherein the at least one of the primers is detectably labeled with a fluorescent label. 
     
     
       9. The method of  claim 6 , wherein the gene expression levels are tested by qRTPCR using primers or probes selected from SEQ ID NO(s): 1-15. 
     
     
       10. The method of  claim 1 , wherein the subject is undergoing myeloma therapy. 
     
     
       11. The method of  claim 1 , which is capable of prognosing OS in a subject undergoing TT2. 
     
     
       12. The method of  claim 1 , which is capable of prognosing both OS and PFS in a subject undergoing TT3a. 
     
     
       13. The method of  claim 1 , which is capable of prognosing PFS in a subject undergoing TT3b. 
     
     
       14. The method of  claim 1 , which is capable of prognosing PFS in a subject undergoing TT4 or TT5. 
     
     
       15. The method of  claim 14 , which is capable of prognosing both OS and PFS in a subject undergoing TT4 or TT5. 
     
     
       16. The method of  claim 1 , which is capable of prognosing OS in a subject undergoing TT6. 
     
     
       17. A method of prognosing progression free survival (PFS) in a subject with multiple myeloma undergoing Total Therapy 3b (TT3b), comprising:
 testing the gene expression levels of enolase 1 (ENO1), fatty acid binding protein 5 (FABP5), thyroid hormone receptor interactor 13 (TRIP13), transgelin 2 (TAGLN2), and replication factor C (activator 1) 4 (RFC4) in a biological sample isolated from the subject; and 
 quantifying the gene expression levels of each of ENO1, FABP5, TRIP13, TAGLN2, and RFC4, 
 wherein an elevated mean, log-normalized gene expression level of ENO1, FABP5, TRIP13, TAGLN2, and RFC4 is associated with a reduced likelihood of PFS for the subject. 
 
     
     
       18. A method of prognosing progression free survival (PFS) or overall survival (OS) in a subject with multiple myeloma undergoing Total Therapy 4 (TT4) or Total Therapy 5 (TT5), comprising:
 testing the gene expression levels of enolase 1 (ENO1), fatty acid binding protein 5 (FABP5), thyroid hormone receptor interactor 13 (TRIP13), transgelin 2 (TAGLN2), and replication factor C (activator 1) 4 (RFC4) in a biological sample isolated from the subject; and 
 quantifying the gene expression levels of each of ENO1, FABP5, TRIP13, TAGLN2, and RFC4, 
 wherein an elevated mean, log-normalized gene expression level of ENO1, FABP5, TRIP13, TAGLN2, and RFC4 as compared to a suitable control for each gene is associated with a reduced likelihood of PFS or OS for the subject. 
 
     
     
       19. The method of  claim 18 , wherein the method is for prognosing OS. 
     
     
       20. The method of  claim 18 , wherein the subject is a human. 
     
     
       21. The method of  claim 18 , wherein the subject exhibits an an elevated mean, log-normalized gene expression level of ENO1, FABP5, TRIP13, TAGLN2, and RFC4 and is thereby determined to have a poor prognosis and is changed to more frequent surveillance schedule. 
     
     
       22. The method of  claim 18 , wherein the subject does not exhibit an elevated mean, log-normalized gene expression level of ENO1, FABP5, TRIP13, TAGLN2, and RFC4 and is thereby determined to have a favorable prognosis. 
     
     
       23. The method of  claim 18 , wherein the subject is undergoing treatment with a proteasome inhibitor, an immunomodulatory drug, cisplatin, etoposide, cyclophosphamide, melphalan, cellular therapy with expanded NK cells, cellular therapy with T-cells, antibody therapy, dexamethasone, and combinations thereof. 
     
     
       24. The method of  claim 18 , wherein the gene expression levels are log-normalized. 
     
     
       25. The method of  claim 18 , wherein a disease index is calculated as the mean of log-normalized gene expression levels of the genes. 
     
     
       26. The method of  claim 18 , wherein the method discriminates between poor and favorable prognosis for OS or PFS with a hazard ratio of at least 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, 3.6, 3.8, 4.0, 4.2, 4.4, 4.6, 4.8, 5.0, 5.2, 5.4, 5.6, 5.8, or 6.0. 
     
     
       27. The method of  claim 18 , wherein the biological sample comprises fewer than 45,000; 40,000; 30,000; 20,000; 10,000; 9,000; 8,000; 7,000; 6,000; 5,000; 4,000; 3,000; 2,000; 1,000; 900; 800; 700; 600; 500; 400; 300; 200; 100; 90; 80; 70; 60; 50; 40; 30; 20; 10; 9; 8; 7; 6; 5; 4; 3; or 2 myeloma cells. 
     
     
       28. The method of  claim 27 , wherein the myeloma cells are selected by CD138 +  expression, CD38 + /CD45 dim  expression, or CD38 + /CD45 neg  expression. 
     
     
       29. A method of prognosing a subject suspected of having multiple myeloma, comprising:
 testing, by qRT-PCR, the nucleic acid gene expression levels of enolase 1 (ENO1), fatty acid binding protein 5 (FABP5), thyroid hormone receptor interactor 13 (TRIP13), transgelin 2 (TAGLN2), and replication factor C (activator 1) 4 (RFC4) in a nucleic acid sample isolated from a biological sample isolated from the subject; and 
 calculating the mean, log-normalized gene expression level of ENO1, FABP5, TRIP13, TAGLN2, and RFC4, 
 wherein an elevated mean, log-normalized gene expression level of ENO1, FABP5, TRIP13, TAGLN2, and RFC4, relative to a suitable control, is associated with a poor prognosis for the subject. 
 
     
     
       30. A method of treating multiple myeloma in a subject, comprising administering a suitable therapy to the subject on the basis of a prognosis by the method of  claim 1 . 
     
     
       31. The method of  claim 1 , wherein the presence of an elevated mean, log-normalized gene expression level of ENO1, FABP5, TRIP13, TAGLN2, and RFC4 is determined using a non-transitory computer-readable storage medium that provides instructions that, if executed by a processor, causes the processor to perform operations comprising:
 reading data representing the gene expression levels of ENO1, FABP5, TRIP13, TAGLN2, and RFC4 determined for an isolated biological sample obtained from a subject; 
 analyzing the data to determine the presence of an elevated mean, log-normalized gene expression level of ENO1, FABP5, TRIP13, TAGLN2, and RFC4 as compared to a suitable control for each gene; and 
 providing a classification of the subject on the basis of the data analysis, wherein the presence of an elevated mean, log-normalized gene expression level of ENO1, FABP5, TRIP13, TAGLN2, and RFC4 is associated with a poor prognosis for the subject.